However, other than these superficial similarities, Tatars and Karaims are very different.

Tatars are Sunni Muslims. They were brought to Lithuania to serve as soldiers, their villages established at the Grand Duchy boundaries and around the capital city Vilnius. The lives of Tatar leaders were somewhat similar to the Catholic nobility. Tatars gradually lost their language and speak Lithuanian natively today, but their Muslim faith survived and continued to distinguish them. Vytautas the Great brought in some 13 000 Tatars, but much less remain today with most Tatar villages disintegrated over the centuries.

An additional influx of Tatars reached Lithuania under the second Soviet occupation (1944-1990) together with other Soviet ethnicities. These Tatars were however largely from the Volga region and may be considered a different ethnicity. Arguably they have more similarities to the Russophones than to the traditional Lithuanian Tatars. In total, there are 3 000 Lithuanian Tatars and Tatars from Volga area. A third of them speak Lithuanian natively, therefore, there may be 1 000 Lithuanian Tatars and the remainder are largely Volga Tatars, two-thirds of whom speak Russian natively.

Tatar heritage in Lithuania includes 4 active mosques (three wooden village ones and a brick one in Kaunas) and Muslim cemeteries in Tatar villages. Surviving Tatar villages are Raižiai (Alytus district municipality), Keturiasdešimt totorių and Nemėžis (both in Vilnius district municipality), but with the exception of the mosques, there is little historical architecture there. Late June every year a traditional ethnic holiday Sabantuy takes place in Trakai. Čeburekai (a Tatar dish used to be taken by soldiers to war) has been appropriated into mainstream Lithuanian cuisine as a popular fast food.

Karaims, on the other hand, practice their own Karaite faith, an offshoot of Judaism. They do not consider themselves to be Jews however and no government that ruled the area did. Even the Nazi German regime did consider Karaims to be a separate ethnicity, sparing them from the Holocaust.

Unlike Tatars, Karaims were always primarily city dwellers rather than soldiers (and in this trait similar to Jews). Initially brought by Vytautas the Great to the Trakai town and Panevėžys area they eventually followed common migration patterns and established their community in Vilnius. However, Trakai remains the heartland of Karaims, and their dishes, such as kibin (Lithuanian: kibinai) pasties or krupnik alcoholic beverage, may be readily tasted in the town.

Interestingly, Karaim cuisine gained a foothold in Lithuania that is far disproportional to the Karaim share of the population. In addition to tasting kibins (pastries with meat) at a local fast food stall, you may investigate Karaim culture in the Karaim museum (Trakai) and two active Kenessas (temples) in Vilnius (Žvėrynas borough) and Trakai. The Karaimų street in Trakai still boasts many homes with traditional three Karaim facade windows.

Unlike Tatars, the Karaims managed to preserve their Turkic language, but their numbers are lower with 2001 census enumerating merely 273 Karaims (138 in Vilnius, 65 in Trakai and 31 in Panevėžys). This is an endangered ethnicity worldwide as even in their Ukrainian homeland there are only some 1 000 of them left.